5M0N

Crystal structure of cytochrome P450 OleT in complex with formate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L40 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277Diffracting crystals were grown in 0.2 M MgCl2, 0.1 M HEPES, 20% PEG 6000, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.17α = 90
b = 60.17β = 90
c = 241.7γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4448.2199.90.03525.812.877736
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.441.471000.6252.96.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4L401.4448.2177736394899.990.136390.134550.17262RANDOM19.786
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.40.4-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.292
r_sphericity_free19.506
r_dihedral_angle_4_deg19.056
r_sphericity_bonded14.285
r_dihedral_angle_3_deg13.902
r_dihedral_angle_1_deg5.804
r_rigid_bond_restr5.332
r_angle_refined_deg2.02
r_angle_other_deg1.072
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.292
r_sphericity_free19.506
r_dihedral_angle_4_deg19.056
r_sphericity_bonded14.285
r_dihedral_angle_3_deg13.902
r_dihedral_angle_1_deg5.804
r_rigid_bond_restr5.332
r_angle_refined_deg2.02
r_angle_other_deg1.072
r_chiral_restr0.133
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_gen_planes_other0.013
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3418
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling